GP-class {AnnBuilder}R Documentation

Class "GP" a sub-class of pubRepo to get/process data from GoldenPath

Description

This class is a sub-class of pubRepo with source specific functions to get/process data from GoldenPath {http://www.genome.ucsc.edu/goldenPath} to obtain gene location and orientation data

Objects from the Class

Objects can be created by calls of the form new("GP", ...). A constructor (GP) is available and should be used to instantiate objects of this class

Slots

organism:
Object of class "character", from class "UG" s character string for the organism of concern
srcUrl:
Object of class "character", from class "UG" a character string for the url where the source data are. As multiple data sources will be used, srcUlr in this case is the location where the source data are (e.g. http://www.genome.ucsc.edu/goldenPath/14nov2002/database/)
parser:
Object of class "character", from class "UG" not in use
baseFile:
Object of class "character", from class "UG" not in use

Extends

Class "UG", directly. Class "pubRepo", by class "UG".

Methods

getStrand
signature(object = "GP"): Processes the refLink and refGene data files and returns a matrix with gene location and orientation data

Note

This class is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

References

http://www.genome.ucsc.edu

See Also

pubRepo-class

Examples

# The example may take a few second to finish
if(interactive()){
  # The url (\url{http://www.genome.ucsc.edu/goldenPath/14nov2002/database/})
  # was correct at the time of coding. Replace with a correct one if it
  # is invalid 
  url <- getSrcUrl("GP", organism = "human")
  gp <- GP(srcUrl = url, organism = "human")
  strand <- getStrand(gp)
}

[Package AnnBuilder version 1.4.21 Index]